\Header{writeToFile}{Writes a textual representation of an exprSetRG
and/or arrayData object}
\keyword{IO}{writeToFile}
\begin{Description}\relax
\code{writeToFile} generates a well-formated
tab-deliminated output file of data
stored in the \code{\Link{exprSetRG}} and/or
\code{\Link{arrayData}} objects.
Different "views" on either a corresponding pair of
an \code{\Link{exprSetRG}}- and an
\code{\Link{arrayData}}-object or of a
single object itself are possible.
The argument \code{channels} allows to specify the "views".
The microarray slide or channel annotation, as well as
the spot annotation is aligned to the data block
if given.
For further restriction and control of the output,
e.g. slide subsets or ordering of slides, you may use
the subsetting operations offered by the
\code{\Link{exprSetRG-class}} and
\code{\Link{arrayData-class}} beforehand
(e.g. slideSubset and [] ).
\end{Description}
\begin{Usage}
\begin{verbatim}writeToFile(arrayDataObject, exprSetRGObject, additionalDataMatrix, rowSelection, slideNameColumn, channels=c("logRatio"), fileName="dumpedData.txt", savePath=".", fullOutput=TRUE, coding=FALSE)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayDataObject}] object of class \code{\Link{arrayData}};
optional/required,
cf. \code{channels}; default: missing
\item[\code{exprSetRGObject}] object of class \code{\Link{exprSetRG}};
optional/required,
cf. \code{channels}; default: missing
\item[\code{additionalDataMatrix}] class \code{matrix}; optional; default: missing.
The rows must correspond to those of the
data objects; \code{colnames} must be supplied.
\item[\code{rowSelection}] vector of indexes; optional; default: missing
\item[\code{slideNameColumn}] character string; optional; default: missing;
must refer to a valid column in
\code{\Link{getHybAttr}}(\code{arrayDataObject})
or in \code{\Link{pDataSlide}}(\code{exprSetRGobject}) 
\item[\code{channels}] vector of character strings; default: \code{c("logRatio")};
valid character strings are:
"logRatio", "green", "red", "rawGreen", "rawRed",
"rawGreenRelative", "rawRedRelative",
"se.exprsLogRatio", "se.exprsGreen", "se.exprsRed".
"Raw"-types must not mix with not "raw"-types and vice versa.
"logRatio"-types must not mix with "colour"-types.
The "raw" types require the argument \code{arrayDataObject},
all other types requires at least the argument \code{exprSetRGObject}.
\item[\code{fileName}] character string; required; default: "dumpedData.txt"
\item[\code{savePath}] character string; required; default: "."
\item[\code{fullOutput}] logical; adds \code{phenoData} information at the top
of the table ; by default: \code{TRUE}
\item[\code{coding}] logical; adds integer-coded-\code{phenoData} information
at the top to the table only if \code{coding = TRUE} and
\code{fullOutput = TRUE}; default: \code{FALSE}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\end{Details}
\begin{Value}
The function is called for its side effect, i.e. writing a file.
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\Link{exprSetRG-class}},
\code{\Link{arrayData-class}},
\code{\Link{write.htmltable}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  
 \end{ExampleCode}
\end{Examples}

